Single-cell RNA sequencing of microglia derived from C9orf72 mutant and isogenic control human iPSCs

This study characterizes transcriptional differences in human iPSC-derived microglia carrying the C9orf72 hexanucleotide repeat expansion (C9) compared to isogenic controls. Overall design: Human iPSCs were differentiated into microglia using a modified version of an established protocol involving embryoid body (EB) formation, hematopoietic induction, and microglial maturation. The differentiation process included sequential exposure to key cytokines and growth factors (BMP4, VEGF, SCF, IL-3, M-CSF, IL-34, and GM-CSF). After 3–4 weeks of maturation, floating microglia-like cells were collected and cultured for terminal differentiation. Single-cell RNA sequencing (scRNA-seq) was then performed to investigate cell-type composition and transcriptional changes associated with the C9orf72 mutation. This dataset enables exploration of C9-related molecular phenotypes in a human microglial context and provides a resource for studying neuroinflammatory mechanisms in ALS/FTD.